@nahisaho/satori 0.15.0 → 0.17.0

package/src/.github/skills/scientific-marine-ecology/SKILL.md

@@ -0,0 +1,429 @@
+---
+name: scientific-marine-ecology
+description: |
+  海洋生態学統合スキル。OBIS 海洋生物分布・WoRMS 海洋分類体系・
+  GBIF 生物多様性レコード・FishBase 魚類データ。ToolUniverse
+  連携: obis, worms, gbif。
+tu_tools:
+  - key: obis
+    name: OBIS (Ocean Biodiversity Information System)
+    description: 海洋生物の出現・分布データを提供する国際プラットフォーム
+  - key: worms
+    name: WoRMS (World Register of Marine Species)
+    description: 海洋生物種の権威ある分類学的参照データベース
+  - key: gbif
+    name: GBIF (Global Biodiversity Information Facility)
+    description: 生物多様性データの国際的なオープンアクセスインフラ
+---
+
+# Scientific Marine Ecology
+
+OBIS / WoRMS / GBIF / FishBase を活用した海洋生物多様性・
+分布解析パイプラインを提供する。
+
+## When to Use
+
+- 海洋生物の地理的分布データを取得するとき
+- 海洋生物の分類学的情報 (WoRMS) を検証するとき
+- 生物多様性ホットスポットを解析するとき
+- 魚類の生態・形態データ (FishBase) を取得するとき
+- 海洋保全区域の生物多様性評価を行うとき
+- 海洋環境変動と種分布の関係を分析するとき
+
+---
+
+## Quick Start
+
+## 1. OBIS 海洋生物分布
+
+```python
+import requests
+import pandas as pd
+import numpy as np
+
+OBIS_BASE = "https://api.obis.org/v3"
+
+
+def obis_occurrence_search(taxon_name=None, taxon_id=None,
+                            geometry=None, year_range=None, limit=1000):
+    """
+    OBIS — 海洋生物出現記録検索。
+
+    Parameters:
+        taxon_name: str — 学名 (例: "Delphinidae")
+        taxon_id: int — AphiaID
+        geometry: str — WKT ジオメトリ (例: "POLYGON((...))")
+        year_range: tuple — (start_year, end_year)
+        limit: int — 最大取得件数
+    """
+    url = f"{OBIS_BASE}/occurrence"
+    params = {"size": min(limit, 5000)}
+
+    if taxon_name:
+        params["scientificname"] = taxon_name
+    if taxon_id:
+        params["taxonid"] = taxon_id
+    if geometry:
+        params["geometry"] = geometry
+    if year_range:
+        params["startdate"] = f"{year_range[0]}-01-01"
+        params["enddate"] = f"{year_range[1]}-12-31"
+
+    resp = requests.get(url, params=params, timeout=60)
+    resp.raise_for_status()
+    data = resp.json()
+
+    records = []
+    for rec in data.get("results", []):
+        records.append({
+            "scientific_name": rec.get("scientificName", ""),
+            "aphia_id": rec.get("aphiaID", ""),
+            "latitude": rec.get("decimalLatitude", None),
+            "longitude": rec.get("decimalLongitude", None),
+            "depth": rec.get("depth", None),
+            "date": rec.get("date_mid", ""),
+            "dataset_id": rec.get("dataset_id", ""),
+            "basis_of_record": rec.get("basisOfRecord", ""),
+        })
+
+    df = pd.DataFrame(records)
+    print(f"OBIS: '{taxon_name or taxon_id}' → {len(df)} occurrences")
+    return df
+
+
+def obis_checklist(geometry=None, area_id=None):
+    """
+    OBIS — 地域別種チェックリスト。
+
+    Parameters:
+        geometry: str — WKT ジオメトリ
+        area_id: int — OBIS エリア ID
+    """
+    url = f"{OBIS_BASE}/checklist"
+    params = {"size": 5000}
+    if geometry:
+        params["geometry"] = geometry
+    if area_id:
+        params["areaid"] = area_id
+
+    resp = requests.get(url, params=params, timeout=60)
+    resp.raise_for_status()
+    data = resp.json()
+
+    species = []
+    for sp in data.get("results", []):
+        species.append({
+            "scientific_name": sp.get("scientificName", ""),
+            "aphia_id": sp.get("taxonID", ""),
+            "records": sp.get("records", 0),
+            "kingdom": sp.get("kingdom", ""),
+            "phylum": sp.get("phylum", ""),
+            "class": sp.get("class", ""),
+            "order": sp.get("order", ""),
+            "family": sp.get("family", ""),
+        })
+
+    df = pd.DataFrame(species)
+    print(f"OBIS checklist: {len(df)} species")
+    return df
+```
+
+## 2. WoRMS 分類学検索
+
+```python
+WORMS_BASE = "https://www.marinespecies.org/rest"
+
+
+def worms_taxon_search(name, fuzzy=True, marine_only=True):
+    """
+    WoRMS — 海洋生物分類学的検索。
+
+    Parameters:
+        name: str — 種名/属名
+        fuzzy: bool — ファジー検索
+        marine_only: bool — 海洋種のみ
+    """
+    url = f"{WORMS_BASE}/AphiaRecordsByName/{name}"
+    params = {
+        "like": str(fuzzy).lower(),
+        "marine_only": str(marine_only).lower(),
+    }
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for taxon in data if isinstance(data, list) else [data]:
+        results.append({
+            "aphia_id": taxon.get("AphiaID", ""),
+            "scientific_name": taxon.get("scientificname", ""),
+            "authority": taxon.get("authority", ""),
+            "status": taxon.get("status", ""),
+            "rank": taxon.get("rank", ""),
+            "valid_name": taxon.get("valid_name", ""),
+            "kingdom": taxon.get("kingdom", ""),
+            "phylum": taxon.get("phylum", ""),
+            "class": taxon.get("class", ""),
+            "order": taxon.get("order", ""),
+            "family": taxon.get("family", ""),
+            "genus": taxon.get("genus", ""),
+            "is_marine": taxon.get("isMarine", 0),
+            "is_brackish": taxon.get("isBrackish", 0),
+            "is_freshwater": taxon.get("isFreshwater", 0),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"WoRMS: '{name}' → {len(df)} taxa")
+    return df
+
+
+def worms_classification(aphia_id):
+    """
+    WoRMS — 完全分類階層取得。
+
+    Parameters:
+        aphia_id: int — AphiaID
+    """
+    url = f"{WORMS_BASE}/AphiaClassificationByAphiaID/{aphia_id}"
+    resp = requests.get(url, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    hierarchy = []
+    node = data
+    while node:
+        hierarchy.append({
+            "aphia_id": node.get("AphiaID", ""),
+            "name": node.get("scientificname", ""),
+            "rank": node.get("rank", ""),
+        })
+        node = node.get("child")
+
+    df = pd.DataFrame(hierarchy)
+    print(f"WoRMS classification: {len(df)} levels")
+    return df
+```
+
+## 3. GBIF 生物多様性レコード
+
+```python
+GBIF_BASE = "https://api.gbif.org/v1"
+
+
+def gbif_species_search(name, limit=20):
+    """
+    GBIF — 種名検索・分類マッチング。
+
+    Parameters:
+        name: str — 種名
+        limit: int — 結果上限
+    """
+    url = f"{GBIF_BASE}/species/search"
+    params = {"q": name, "limit": limit}
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for sp in data.get("results", []):
+        results.append({
+            "taxon_key": sp.get("key", ""),
+            "scientific_name": sp.get("scientificName", ""),
+            "canonical_name": sp.get("canonicalName", ""),
+            "status": sp.get("taxonomicStatus", ""),
+            "rank": sp.get("rank", ""),
+            "kingdom": sp.get("kingdom", ""),
+            "phylum": sp.get("phylum", ""),
+            "class": sp.get("class", ""),
+            "order": sp.get("order", ""),
+            "family": sp.get("family", ""),
+            "num_occurrences": sp.get("numOccurrences", 0),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"GBIF species: '{name}' → {len(df)} taxa")
+    return df
+
+
+def gbif_occurrence_search(taxon_key=None, country=None,
+                            year_range=None, limit=300):
+    """
+    GBIF — 出現記録検索。
+
+    Parameters:
+        taxon_key: int — GBIF taxon key
+        country: str — ISO 国コード (例: "JP")
+        year_range: tuple — (start, end)
+        limit: int — 最大件数
+    """
+    url = f"{GBIF_BASE}/occurrence/search"
+    params = {"limit": min(limit, 300)}
+
+    if taxon_key:
+        params["taxonKey"] = taxon_key
+    if country:
+        params["country"] = country
+    if year_range:
+        params["year"] = f"{year_range[0]},{year_range[1]}"
+
+    resp = requests.get(url, params=params, timeout=60)
+    resp.raise_for_status()
+    data = resp.json()
+
+    records = []
+    for rec in data.get("results", []):
+        records.append({
+            "gbif_id": rec.get("gbifID", ""),
+            "scientific_name": rec.get("scientificName", ""),
+            "latitude": rec.get("decimalLatitude", None),
+            "longitude": rec.get("decimalLongitude", None),
+            "country": rec.get("country", ""),
+            "year": rec.get("year", ""),
+            "basis_of_record": rec.get("basisOfRecord", ""),
+            "institution": rec.get("institutionCode", ""),
+        })
+
+    df = pd.DataFrame(records)
+    print(f"GBIF occurrences: {len(df)} records (total: {data.get('count', 0)})")
+    return df
+```
+
+## 4. FishBase 魚類データ
+
+```python
+FISHBASE_BASE = "https://fishbase.ropensci.org"
+
+
+def fishbase_species(genus=None, species=None, family=None):
+    """
+    FishBase — 魚類種データ取得。
+
+    Parameters:
+        genus: str — 属名
+        species: str — 種小名
+        family: str — 科名
+    """
+    url = f"{FISHBASE_BASE}/species"
+    params = {"limit": 100}
+    if genus:
+        params["Genus"] = genus
+    if species:
+        params["Species"] = species
+    if family:
+        params["Family"] = family
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    records = []
+    for fish in data.get("data", []):
+        records.append({
+            "spec_code": fish.get("SpecCode", ""),
+            "genus": fish.get("Genus", ""),
+            "species": fish.get("Species", ""),
+            "family": fish.get("Family", ""),
+            "body_shape": fish.get("BodyShapeI", ""),
+            "max_length": fish.get("Length", None),
+            "vulnerability": fish.get("Vulnerability", None),
+            "importance": fish.get("Importance", ""),
+            "habitat": fish.get("DemersPelag", ""),
+            "depth_range": f"{fish.get('DepthRangeShallow', '')}-{fish.get('DepthRangeDeep', '')}",
+        })
+
+    df = pd.DataFrame(records)
+    print(f"FishBase: {len(df)} species")
+    return df
+```
+
+## 5. 海洋生態学統合パイプライン
+
+```python
+def marine_ecology_pipeline(taxon_name, region_wkt=None,
+                             output_dir="results"):
+    """
+    OBIS + WoRMS + GBIF + FishBase 統合パイプライン。
+
+    Parameters:
+        taxon_name: str — 分類群名
+        region_wkt: str — 調査海域 WKT
+        output_dir: str — 出力ディレクトリ
+    """
+    from pathlib import Path
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # 1) WoRMS 分類検証
+    taxonomy = worms_taxon_search(taxon_name)
+    taxonomy.to_csv(output_dir / "worms_taxonomy.csv", index=False)
+
+    aphia_id = None
+    if len(taxonomy) > 0:
+        aphia_id = taxonomy.iloc[0]["aphia_id"]
+        classification = worms_classification(aphia_id)
+        classification.to_csv(output_dir / "classification.csv", index=False)
+
+    # 2) OBIS 海洋分布
+    obis_data = obis_occurrence_search(
+        taxon_name=taxon_name,
+        taxon_id=aphia_id,
+        geometry=region_wkt,
+    )
+    obis_data.to_csv(output_dir / "obis_occurrences.csv", index=False)
+
+    # 3) GBIF 補完
+    gbif_sp = gbif_species_search(taxon_name)
+    if len(gbif_sp) > 0:
+        taxon_key = gbif_sp.iloc[0]["taxon_key"]
+        gbif_occ = gbif_occurrence_search(taxon_key=taxon_key)
+        gbif_occ.to_csv(output_dir / "gbif_occurrences.csv", index=False)
+    else:
+        gbif_occ = pd.DataFrame()
+
+    # 4) 多様性指標
+    if len(obis_data) > 0:
+        n_species = obis_data["scientific_name"].nunique()
+        lat_range = (obis_data["latitude"].min(), obis_data["latitude"].max())
+        depth_range = (obis_data["depth"].min(), obis_data["depth"].max())
+        print(f"Diversity: {n_species} species, "
+              f"lat {lat_range}, depth {depth_range}")
+
+    print(f"Marine ecology pipeline: {output_dir}")
+    return {
+        "taxonomy": taxonomy,
+        "obis_occurrences": obis_data,
+        "gbif_occurrences": gbif_occ,
+    }
+```
+
+---
+
+## ToolUniverse 連携
+
+| TU Key | ツール名 | 連携内容 |
+|--------|---------|---------|
+| `obis` | OBIS | 海洋生物出現・分布レコード検索 |
+| `worms` | WoRMS | 海洋種分類学的検証・階層取得 |
+| `gbif` | GBIF | 生物多様性出現レコード検索 |
+
+## パイプライン統合
+
+```
+environmental-ecology → marine-ecology → phylogenetics
+  (陸域生態学)          (OBIS/WoRMS/GBIF)  (系統解析)
+       │                      │               ↓
+  biodiversity-db ───────────┘         species-distribution
+  (ENA/BOLD)           │               (空間分布モデル)
+                       ↓
+                  fisheries-management
+                  (水産資源管理)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/worms_taxonomy.csv` | WoRMS 分類情報 | → phylogenetics |
+| `results/obis_occurrences.csv` | OBIS 出現記録 | → species-distribution |
+| `results/gbif_occurrences.csv` | GBIF 出現記録 | → biodiversity-db |
+| `results/classification.csv` | 分類階層 | → environmental-ecology |

package/src/.github/skills/scientific-metabolic-atlas/SKILL.md

@@ -0,0 +1,263 @@
+---
+name: scientific-metabolic-atlas
+description: |
+  代謝アトラススキル。Metabolic Atlas / Human-GEM REST API による
+  代謝反応・代謝産物・コンパートメント検索、フラックス解析統合、
+  代謝ネットワーク可視化。K-Dense 連携: metabolic-atlas。
+tu_tools: []
+kdense_ref: metabolic-atlas
+---
+
+# Scientific Metabolic Atlas
+
+Metabolic Atlas REST API を活用したゲノムスケール代謝モデル
+(GEM) 解析パイプラインを提供する。
+
+## When to Use
+
+- ヒト代謝反応・代謝産物を検索するとき
+- Human-GEM のコンパートメント情報を取得するとき
+- 代謝経路のネットワーク構造を解析するとき
+- フラックスバランス解析 (FBA) の入力を準備するとき
+- 代謝産物コネクティビティを可視化するとき
+- 組織特異的代謝モデルを構築するとき
+
+---
+
+## Quick Start
+
+## 1. 代謝反応検索
+
+```python
+import requests
+import pandas as pd
+import numpy as np
+
+MA_BASE = "https://metabolicatlas.org/api/v2"
+
+
+def metabolic_atlas_search_reactions(query, model="Human-GEM",
+                                       compartment=None, limit=50):
+    """
+    Metabolic Atlas — 代謝反応検索。
+
+    Parameters:
+        query: str — 検索クエリ (例: "glycolysis", "citrate")
+        model: str — GEM モデル名
+        compartment: str — コンパートメント (例: "cytosol", "mitochondria")
+        limit: int — 最大結果数
+    """
+    url = f"{MA_BASE}/search"
+    params = {
+        "query": query,
+        "model": model,
+        "type": "reaction",
+        "limit": limit,
+    }
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for r in data.get("results", data) if isinstance(data, dict) else data:
+        rxn = r if isinstance(r, dict) else {}
+        row = {
+            "reaction_id": rxn.get("id", ""),
+            "name": rxn.get("name", ""),
+            "equation": rxn.get("equation", ""),
+            "subsystem": rxn.get("subsystem", ""),
+            "compartment": rxn.get("compartment", ""),
+            "gene_rule": rxn.get("geneRule", ""),
+            "lower_bound": rxn.get("lowerBound", None),
+            "upper_bound": rxn.get("upperBound", None),
+        }
+        if compartment and compartment.lower() not in str(
+                row.get("compartment", "")).lower():
+            continue
+        results.append(row)
+
+    df = pd.DataFrame(results[:limit])
+    print(f"Metabolic Atlas reactions: {len(df)} results "
+          f"(query={query})")
+    return df
+```
+
+## 2. 代謝産物検索
+
+```python
+def metabolic_atlas_search_metabolites(query, model="Human-GEM",
+                                          limit=50):
+    """
+    Metabolic Atlas — 代謝産物検索。
+
+    Parameters:
+        query: str — 検索クエリ (例: "glucose", "ATP")
+        model: str — GEM モデル名
+        limit: int — 最大結果数
+    """
+    url = f"{MA_BASE}/search"
+    params = {
+        "query": query,
+        "model": model,
+        "type": "metabolite",
+        "limit": limit,
+    }
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for m in data.get("results", data) if isinstance(data, dict) else data:
+        met = m if isinstance(m, dict) else {}
+        results.append({
+            "metabolite_id": met.get("id", ""),
+            "name": met.get("name", ""),
+            "formula": met.get("formula", ""),
+            "charge": met.get("charge", None),
+            "compartment": met.get("compartment", ""),
+            "chebi_id": met.get("chebiId", ""),
+            "kegg_id": met.get("keggId", ""),
+        })
+
+    df = pd.DataFrame(results[:limit])
+    print(f"Metabolic Atlas metabolites: {len(df)} results "
+          f"(query={query})")
+    return df
+```
+
+## 3. 代謝ネットワーク解析
+
+```python
+import networkx as nx
+
+
+def metabolic_atlas_network(subsystem, model="Human-GEM"):
+    """
+    Metabolic Atlas — サブシステム代謝ネットワーク構築。
+
+    Parameters:
+        subsystem: str — サブシステム名 (例: "Glycolysis")
+        model: str — GEM モデル名
+    """
+    reactions = metabolic_atlas_search_reactions(
+        subsystem, model=model, limit=200)
+
+    G = nx.DiGraph()
+
+    for _, rxn in reactions.iterrows():
+        rxn_id = rxn["reaction_id"]
+        equation = str(rxn.get("equation", ""))
+
+        # 簡易パーサ: "A + B => C + D"
+        if "=>" in equation:
+            substrates_str, products_str = equation.split("=>", 1)
+        elif "=" in equation:
+            substrates_str, products_str = equation.split("=", 1)
+        else:
+            continue
+
+        substrates = [s.strip() for s in substrates_str.split("+")
+                       if s.strip()]
+        products = [p.strip() for p in products_str.split("+")
+                     if p.strip()]
+
+        G.add_node(rxn_id, type="reaction",
+                    name=rxn.get("name", ""))
+
+        for s in substrates:
+            G.add_node(s, type="metabolite")
+            G.add_edge(s, rxn_id)
+
+        for p in products:
+            G.add_node(p, type="metabolite")
+            G.add_edge(rxn_id, p)
+
+    # ネットワーク統計
+    n_reactions = sum(1 for _, d in G.nodes(data=True)
+                      if d.get("type") == "reaction")
+    n_metabolites = sum(1 for _, d in G.nodes(data=True)
+                         if d.get("type") == "metabolite")
+
+    print(f"Metabolic network: {n_reactions} reactions, "
+          f"{n_metabolites} metabolites, {G.number_of_edges()} edges")
+    return G
+```
+
+## 4. 代謝アトラス統合パイプライン
+
+```python
+def metabolic_atlas_pipeline(query, model="Human-GEM",
+                               output_dir="results"):
+    """
+    代謝アトラス統合パイプライン。
+
+    Parameters:
+        query: str — 代謝経路/サブシステム名
+        model: str — GEM モデル名
+        output_dir: str — 出力ディレクトリ
+    """
+    from pathlib import Path
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # 1) 反応検索
+    reactions = metabolic_atlas_search_reactions(query, model=model)
+    reactions.to_csv(output_dir / "reactions.csv", index=False)
+
+    # 2) 代謝産物検索
+    metabolites = metabolic_atlas_search_metabolites(query, model=model)
+    metabolites.to_csv(output_dir / "metabolites.csv", index=False)
+
+    # 3) ネットワーク構築
+    G = metabolic_atlas_network(query, model=model)
+    nx.write_graphml(G, str(output_dir / "metabolic_network.graphml"))
+
+    # 4) ハブ代謝産物
+    met_nodes = [n for n, d in G.nodes(data=True)
+                  if d.get("type") == "metabolite"]
+    hub_scores = {n: G.degree(n) for n in met_nodes}
+    hub_df = pd.DataFrame([
+        {"metabolite": k, "degree": v}
+        for k, v in sorted(hub_scores.items(),
+                           key=lambda x: -x[1])[:20]
+    ])
+    hub_df.to_csv(output_dir / "hub_metabolites.csv", index=False)
+
+    print(f"Metabolic Atlas pipeline: {output_dir}")
+    return {
+        "reactions": reactions,
+        "metabolites": metabolites,
+        "network": G,
+        "hubs": hub_df,
+    }
+```
+
+---
+
+## K-Dense 連携
+
+| K-Dense Key | 参照内容 |
+|-------------|---------|
+| `metabolic-atlas` | 代謝モデル構造・反応データベース |
+
+## パイプライン統合
+
+```
+metabolic-modeling → metabolic-atlas → systems-biology
+  (COBRA/FBA)        (Human-GEM)       (統合モデリング)
+       │                   │                  ↓
+  pathway-enrichment ─────┘          gene-expression
+  (KEGG/Reactome)     │              (発現データ)
+                       ↓
+                 multi-omics
+                 (メタボロミクス統合)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/reactions.csv` | 代謝反応一覧 | → metabolic-modeling |
+| `results/metabolites.csv` | 代謝産物一覧 | → pathway-enrichment |
+| `results/metabolic_network.graphml` | 代謝ネットワーク | → systems-biology |
+| `results/hub_metabolites.csv` | ハブ代謝産物 | → multi-omics |